Biochemistry

Biochemistry

44 BIOCHEMICAL EDUCATION REVIEW ESSAY July 1975 Vol. 3 No. 3 I Biochemistry STANLEY DAGLEY By L u b e r t Stryer. 1975. 8 7 7 p a g e s a n d 6...

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44

BIOCHEMICAL EDUCATION

REVIEW ESSAY

July 1975 Vol. 3 No. 3

I

Biochemistry

STANLEY DAGLEY

By L u b e r t Stryer. 1975. 8 7 7 p a g e s a n d 626 i l l u s t r a t i o n s . W. H. Freeman and Company, San Francisco. $19.95. New textbooks that cover the general area of biochemistry are published at regular intervals of time, and as each one appears I usually feel some curiosity concerning this fresh manifestation of energy. W h a t justifies the considerable effort involved in writing a new textbook? Let us leave financial consideration aside: indeed, m a n y authors would agree that you might just as well do this, although I have yet to meet a publisher in the same frame of mind. Clearly, a new book may be justified if an author has new things to say; but not, I feel, if the text simply reiterates old themes and relies upon artistic embellishment to catch the eye and hold the attention. Now, one can open this book almost at any page and discover a brilliant example of artistic expression used to illuminate scientific concepts. But in addition, the author has an attractive style of writing; and most important, he has something new to say. Despite its price, this book will survive a n d succeed. A constant supply of textbooks in excess of requirements has set in motion a process analogous to evolution through which those works survive that are best fitted to satisfy what readers believe to be their needs. Some surprising m u t a n t s have appeared and persisted in the world of learning. I suppose that the most remarkable was the book of Edward Hyde, first Earl of Clarendon and chancellor to Charles II, which goes by the abbreviated title of A History of the Rebellion. Editions were published throughout two centuries, the 18th and 19th, and early profits were used to erect a building in 1721 to house the university press at Oxford where Hyde had also served as chancellor. Later, his great-grandson left manuscripts with which he intended to fund an academy for horse-riding and other exercises; but in 1868 the money was used to establish the Clarendon Laboratory. Even an Oxford scientist might be permitted a twinge of regret for the opportunity lost to start a new and exciting university discipline (to use the jargon of modern education), and he might also perceive the first step in the direction of the Cowley motor works. I understand that Clarendon's History has some shortcomings as a record of facts, but there is no doubt that it fed and satisfied the prejudices of the readers. For th[ following reasons I believe that the same is true of scientific best-sellers. The least valuable of all 20th century obiter dicta is Henry Ford's "History is b u n k " ; for it is easy enough, without encouragement from spurious generalizations, to lose sight of the fact that our traditional presentation of general biochemistry has been influenced by intellectual fashions and by the time-sequence of successful research; and that this, in turn, is the research deemed worthy of support by influential contemporaries who also largely decide the areas in which students shall be trained for the future. Anyone who doubts the influence of fashion and prejudice on the progress of science should ponder the treatment received by T h u d i c h u m and M c M u n n separately at the h a n d s of the nineteenth century scientific establishment. Incidentally, it is encouraging to note that in the case of T h u d i c h u m the Biochemical Society has followed the example of Callixtus III who absolved Joan of Arc posthumously from all taint of heresy. The establishment of a memorial lecture is the scientific counterpart of canonization. I believe, then, that the development of biochemistry in the past has been influenced by many purely h u m a n factors. Moreover, at the present time, a good overall evaluation of the vast range of observations accumulated by biochemists calls for the exercise of j u d g e m e n t analogous to that shown by a responsible historian when he surveys a complex record of h u m a n affairs. The main highway

across known biochemical territory is not the only one that might have been taken, h a d events been otherwise. It is now possible to admire the scene from several points of vantage; and indeed there are some satisfying views that have never been described at all. The evolutionary process for textbooks in general biochemistry will therefore continue not only because new observations proliferate, but mainly because of increased scope for new interpretations and emphases. Since I believe that Lubert Stryer's book will survive competition, I should mention the new things he has to say. His exposition is organized around several major themes: conformation-exemplified by the relationship between threedimensional structure of proteins and their biological activity; generation and storage of metabolic energy; biosynthesis of macromolecular precursors; genetic information; and molecular physiology - - interaction of information, conformation and metabolism. The last section is particularly attractive, display~_ng m u c h originality in presentation. This section, and the chapters on eucaryotic chromosomes, viruses and immunoglobulins contain some of the best illustrations I have ever seen in a textbook; indeed, the author displays a genius for integrating words and pictures. This, and freshness of style, makes the book easy to read: thus, those who enjoy music can see a passage from J. S. Bach compared with the basic structural design of a collagen fiber on page 217. l was intrigued by the unobtrusive way that the reader is made aware that research is done by people: about 180 are mentioned, and their first n a m e s given in the vast majority of cases. The only person I noticed with neither initials nor first n a m e was Rasputin. But his scientific contributions have generally been considered to be negligible, except by one candidate I once examined who gave him credit for having been the first to draw up the periodic table of the chemical elements. W h a t of more traditional approaches? Like most successful general texts written since the first edition of Baldwin's Dynamic Aspects of Biochemistry, m u c h of metabolism is discussed in terms of energy-rich compounds. This approach is valuable for those who know what they are talking about, but it can be easily misinterpreted by those whose chemical background is inadequate. At a symposium on education held at the FABS meeting in April I showed nine slides of statements and diagrams from (unidentified) textbooks of biology published over the last seven years. They included the following: (1) "If the phosphate bonds in the diphosphate are separated one at a time from the sugar or alcohol and the heat loss is measured, it is found that the first phosphate bond added to R is E-poor and the second is E-rich. The E-poor bond equals 3000 calories - while the E-rich contains 8000 calories - - " . (2) "Glucose is a relatively stable compound. If its chemical bond energy is to be released, the glucose molecule must be made more reactive. The energy required for this purpose, termed activation energy is available from ATP within the cell". I dare say that the volumes containing these statements are already extinct lines in textbook evolution, but the following is from a survivor that achieved a recent second edition: (3) - - " b o n d energy is released in the form of one or more highly energized electrons. The electrons can be passed along, usually each with an accompanying proton (a hydrogen ion) from acceptor to acceptor, releasing energy at every exchange". I was left speculating as to whether the electrons moved in ever-diminishing circles, and where it was that they finally disappeared. Now there are no misconceptions of this, or any other sort, in

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Lubert Stryer's book. On the contrary, his account of free energy is clear and accurate, and he wtrns against some wrong ideas fostered by half-understood 'thermodynamic functions. But it remains my opinion, which I have expressed before 1, that for yo~:ng students, emphasis on energetics has tended to encourage neglect of elementary principles of chemical reactivity which are no less valuable, to say the least. Not all biochemists disagree with me, since one eminently worthy survivor of prevailing competition is Conn and Stumpf's Outlines o f Biochemistry (3rd ed.) which stresses this approach. I agree that it is very satisfying to pereeive how structure and function in biology relate to the shape of macromolecular components. But it is equally rewarding to be able to appreciate that the chemical structures of coenzymes such as pyridoxal phosphate and thiamine pyrophosphate are exquisitely appropriate for accommodating the ebb and flow of electrons in enzymecatalyzed reactions. The phosphorylations that occur when farnesyl pyrophosphate is synthesized fulfil the usual demand of a biosynthetic pathway for an input of free energy, but a student can gain a far better appreciation of how this molecule is assembled if he has been taught that nature uses chemical reagents that possess phosphate and pyrophosphate groups which then serve as leaving groups to generate electrophilic sites. L. Ruzicka z has diagrammed this particular pathway in a clear and simple manner that is eminently suitable for presentation to beginners. Of all the metabolic routes that seem to consist of dull and pointless reactions at first, and suddenly appear to be ingenious and satisfying in the light of electronic shifts, the most striking examples are to be found in the area of aromatic biosynthesis. There is one large section of biochemistry that is not covered in this book, nor in any other general text. It should form part of the education of a modern biologist, and its importance for society has been recognized most belatedly. I refer to the operation of the carbon cycle and a related topic, the biochemistry of oxygen gas. This is one aspect of the biochemical scenery, as I mentioned earlier, that is never admired; and the reasons for this neglect are historical. As our science developed it was inevitable that it should focus on Man. Of course much attention was also given to ~. co/i, but chiefly because it was a convenient system to work with, that told us indirectly of what takes place in Man, rather than what takes place in microbes. Now, in the slow and majestic processes of the carbon cycle, degradation is as important as biosynthesis, although the latter has received far more attention from biochemists. Vast quantities of material that are biochemically inert for higher organisms are synthesized by plants and can only be degraded by microbes. Without this activity, the carbon cycle would grind to a half. Commensurate with their role, the total mass of microbes far exceeds the total mass of animals; but their mass is inversely proportional to the amount of attention they receive. And linked inevitably with this neglect, goes neglect of that vital component of our biosphere, molecular oxygen. The metabolic maps that we hang on the walls of our offices summarize those central biochemical reactions that we consider to be most worthy of record. The vast majority of oxidations and reductions shown on the map will be transfers of hydrogen mediated by pyridine nucleotides. These are processes common to all living forms. The|r origins may well be rooted in those conditions that prevailed on Earth before oxygen gas made its appearance in the atmosphere. But as for its participation now, the metabolic map shows the collection of hydrogen by NAD, its transfer to the electron transport chain usually placed at the bottom of the map, and then at last oxygen enters the picture. It is shown combining with protons and electrons to form a pool of water on the floor at the bottom of the map. This seems to me to be a trivial assignment (another adjective is suggested by the pool of water) for the element whose unique properties made the evolution of Man possible. These properties are evident, briefly, in the sluggish reactivity of the oxygen molecule towards carbon compounds under physiological conditions, and

in the thermodynamic stability of carbon dioxide in the present atmosphere of the earth. The second commonest polymer in nature, and the most neglected, is lignin. Some of the chemical links in this inert molecule, and in thousands of other natural products, are only likely to be broken by the action of oxygenases possessed by micro-organisms. As we try to understand how the carbon cycle is maintained in operation, and how man's chemical insults to his environment might be redressed or avoided, we shall discover many new and specific enzymes of this type that activate molecular oxygen. This activation is a very hazardous process 3 which aerobic microbes have managed to bring safely under control. The number of oxygenases may eventually rival that of known dehydrogenases, but I hope we do not have to wait to see whether this is true before we start to teach students about such basic chemical features of the biosphere. Millions of tons of carbon, sequestered by plants as relatively inert metabolic structures, are released annually for use in the biosphere by microbial reactions that fix oxygen. It may be true that, excepting cytychrome P450, medical students need not be told about them. But as for biologists, and indeed mankind in general, the time has come for educators to provide them with alternatives to slogans and emotion, and to show that there are rational biochemical approaches to problems of the environment. I strongly recommend Lubert Stryer's book. It is beautifully presented and, as the reader will realize, it stimulated me to reflect again upon the pleasures and problems of teaching general biochemistry. The artistry and freshness of the book reminded me of a youthful conviction (some would say delusion) that the world of nature is beautiful and also makes sense. As Hinshelwood remarked of human understanding4: "without poetry it loses colour, without art immediacy and without science it loses structure and coherence". My criticisms of this book on points of science or nomenclature are minor. I would prefer the book to follow the recommendations of the Enzyme Commission in two respects. First, the name oxidase should be used only for cases where Oz acts as an acceptor of hydrogen; and oxygenase used when atoms of oxygen are incorporated directly into the substrate. For example, L-amino acid oxidase in contrast to homogentisate 1,2dioxygenase. Second, the enzyme involved in the process of transporting acetyl groups across mitochondrial membranes is best described as ATP citrate lyase (E.C. 4.1.3.8) to distinguish it from the bacterial enzyme citrate lyase (E.C. 4.1.3.6). The latter enzyme is still the object of much interesting research by groups working with G. Gottschalk in G6ttingen and P. A. Srere in Dallas. The impression conveyed on page 326, that ATP is an important allosteric regulator of the Krebs cycle by virtue of its action on citrate synthase, would be strongly disputed by some workers s. Also, the possibility that cholesterol biosynthesis may be partly regulated by direct inhibition of 3hydroxy-3-methylglutaryl CoA reductase activity (page 492) should not be ruled out 6. In discussing the catabolism of branched chain amino acids (page 450) it is stated that isoleucine yields propionyl CoA whereas valine yields methylmalonyl CoA. Most textbooks show this: propionyl CoA is formed from isoleucine and then gives (S)-methylmalonyl CoA, so that the two catabolic pathways join at this compound. Actually, there is very good evidence7 that propionyl CoA is formed on both pathways: thus, methylmalonate semialdehyde is formed from valine and is then oxidized directly to propionyl CoA by a CoA-dependent dehydrogenase. Methylmalonyl CoA is therefore common to both pathways but is formed after propionyl CoA in each case. On page 506, the serine hydroxymethyl transferase reaction is shown, as it is in most textbooks and also in the most recent publication of the Enzyme Commission s , without the participation of water that stoichiometry requires. This can be confusing to the careful student. The numbering of the carbon atoms in the ring system of shikimic acid (page 511) is not in accordance with modern conventionsg, although it must be admitted that in this case the

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old numbering (which is in line with that used for quinic acid) is less baffling to a student than is the new. Finally, although there are overwhelming arguments for retaining the designations D- and L- for amino acids and sugars, there are some biochemicals to which the Sequence Rule t° should be applied instead. In any case, students will not be able to understand modern papers concerned with enzymic mechanisms that involve stereochemistry unless they have mastered this rule. Its value is seen when one considers the structures for the isomers of methylmalonyl CoA on page 444. These are correct, and are designated as D and L by placing the free carboxyl group at the top of each projection formula, and the esterified carboxyl at the bottom. However, on page 417 the structure of the biologically-active isomer of 3-hydroxy-3-methylglutaryl CoA is again shown correctly (but is not designated) by placing the free carboxyl group at the bottom and the esterified carboxyl at the top. Students usually ask for a rule on these matters; and Cahn et al. 1° have provided them with one. They ought to use it.

REFERENCES 1

S. Dagley, Biochem. Education (1974).

1, 4 (1972); ibid 2, 16

Genetics a n d Biochemistry of Pseudomonas E d i t e d by P. H . C l a r k e a n d M . H. R i c h m o n d . P p . 366. J o h n Wiley a n d Sons, 1975. £14.00. Bacteria of the genus Pseudomonas have long been of interest to biochemists because of their remarkable versatility in catabolising esoteric organic compounds. Recently, the genes for enzymes mediating some of these pathways have been shown to lie on plasmids (which may be transmissible via conjugation) rather than on the bacterial chromosome. Also over the last few years, Pseudomonas aeruginosa has assumed importance as an opportunistic human pathogen, especially in burns, one of its characteristics being a high intrinsic level of resistance to most antibiotics; and an isolate from such a source provided the first example of a transmissible antibiotic resistance factor in a group outside the enterobacteria. For these reasons, the organisms are being studied more extensively than ever by bacterial biochemists and geneticists. This book attempts to review these areas of current interest. It comprises nine essays by scientists who have made important contributions in these fields. Palleroni contributes a description of the properties and taxohomy of the genes, stressing especially modern biochemically-based aspects of the latter. Lowbury discusses medical aspects of P. aeruginosa. Meadow gives an account of wall and membrane structures. Holloway describes (with Krishnapillai) bacteriophages and bacteriocins, and (on his own) genetic organisation; Stanisich and Richmond then proceed with a contribution on gene transfer. There follow two chapters by Clarke and Ornston on metabolic pathways and regulation. Finally, Clarke and Richmond estimate the evolutionary prospects for the genus. The standard of exposition is high throughout. Although there is necessarily much detail, this is clearly presented and the reader's gaze is directed to the wood as well as the trees. In the genetic sections, a familiarity with standard (i.e. enterobacterial) prokaryote genetics is not assumed, which will help readers who are primarily biochemists. Overlap, hard to avoid in such a multi-author treatise, is minimal (it is most noticeable between the chapters .by Holloway and by Stanisich and Richmond). There is a sprinkling of misprints, mostly in short words so that the reader is unlikely to be misled. The index is good. It seems that a growth area of bacterial genetics in the near future will be the detailed study of groups outside the enterobacteria, such as the genus Pseudomonas. This volume is therefore likely to be a popular and timely source book, and can

July 1975 Vol. 3 No. 3

2

L. Rhzick~, Ann. Rev. Biochem. 43, 15 (1973).

3

I. Fridovich, Horizons in Biochem. Biophys. 1, 1 (1974).

4

C. N. Hinshelwood, 15th Eddington Memorial Lecture, Cambridge University Press, page 32 (1961).

5

G . W . Kosicki and L. P. K. Lee, J. Biol. Chem. 241, 3521 (1966); K. F. LaNoue, J.Bryla and J. R. Williamson, ibid 247, 667 (1972). See also a review: B. A. C. Ackrell, Horizons in Biochem. Biophys. 1, 188 (1974).

s

M. Higgins and H. Rudney, Nature New Biol. 246, 60 (1973).

7

J. R. Sokatch, L. E. Saunders and V. P. Marshall, J. Biol. Chem. 243, 2500 (1968); also, R. R. Martin, V. P. Marshall, J. R. Skotach and L. Unger, J. Bacteriol. 115, 198 (1973).

s

Enzyme Nomenclature (1972). Elsevier Publ. Co., page 126.

9

B . A . Bohm, Chem. Rev. 65, 435 (1965).

10 R. S. Cahn, C. K. Ingold and V. Prelog, Experientia 12, 81 (1956). See also R. S. Cahn, J. Chem. Education 41, 116 (1964).

be recommended to the final year undergraduate, the postgraduate student, and the research worker alike. A companion volume, Resistance in Pseudomonas, edited by Professor M. R. W. Brown, is promised by the publishers later this year. The price seems exorbitant, but I suppose no-one is expecting individuals to buy copies. Department of Genetics, S. Baumberg University of Leeds, U.K.

Collection de B i o c h i m i e By Pierre Louisot. Biochimle Structurale 2. Acid Nucl~iques, 2nd Ed. 1974, iv + 48 pp. 3. Vitamlnes, Coenzymes, 2nd Ed. 1974, 104 pp. 4. Lipides et D6riv6s lsopr6niques, 2 n d E d . 1974, 89 p p . SIMEP Editions, 69611-Villeurbanne, France. All 210 x 270 m m . These books are revisions of some of the parts of the whole Collection de Biochimie by Dr Louisot that was reviewed previously (Biochemical Education, 1974, 2, 34). The opportunity has been taken to include some additional information, for example, the sequencing of nucleic acids, the RNA viruses, tRNA, ribosomal RNA, and the nucleases are dealt with more fully. In the volume on vitamins there are new sections on the biosyntheses of several of them, there is more about their classification and mechanisms of action. There is a new diagram of mitochondriai structure and more on the spectra and structure of cytochromes. An amusing note is included about the sex-change that has overtaken the word enzyme in French. "It was mainly feminin from 1925 to 1930, then principally masculin and since 1935 it has always been used in the masculin gender. The Acad6mie Franeaise remains, we are told, firmly in favour of the gentler sex. The presentation is better than that of the previous edition. The type looks more 'modern', less use is made of very dark headings, and the diagrams are often smaller but still legible, some have been redrawn. Each volume now has a subject index. The series should continue to be very useful to students. Department of Biochemistry University College London WCIE 6BT

S . P . Datta